P500-M genome project opens int’l linkages
by Melody M. Aguiba
May 10, 2014
The government’s genome project, now valued at around P500 million, is seen paving the way to Philippines’ international collaboration on research on cancer and other diseases such as potentially with the United States’ National Institutes of Health (NIH).
A new bioinformatics core facility, opened last April, will support these collaborative programs. The genome project is co-funded by the Philippine Council for Health Research and Development and Department of Science and Technology.
The genome project has already started research on prevalent diseases in the country including
dengue, diabetes, and cardiovascular diseases. It is further encouraging collaborations with the private sector and academic institutions.
“The Philippine Genome Center (PGC) is for any researcher in the country who wants to do genomics research for the benefit of the Filipino,” said PGC Executive Director Carmencita D. Padilla said in an interview at the bioinformatics facility launch.
A potential international collaboration is with the National Center for Advancing Translational Sciences (NCATS) of the US’s NIH. NCATS is currently conducting a five-year program on Bioengineered Organs-on-Chips Disease Modeling and Drug Development program.
Guest at the bioinformatics facility launch was NCATS-NIH’s Danilo A. Tagle.
“At the end of five years, it is anticipated that the availability of these systems to a broader research community will foster a multitude of new research applications including in personalized medicine, reproduction and development, infectious diseases, cancer,” said Tagle.
Other applications of bioengineered organs-on-chips, according to Tagle, are in countermeasures for chemical warfare, immune responses, and neuro-inflammation. Organs-on-chips bioengineering involves use of devices that do simulation of the functions of real human organs in order to predict effects of certain therapies.
An example is a model of a breathing lung on a microchip which employs the use of living human lung cells integrated into the computer chip technology.
“This device mimics how the lung works so that scientists can more accurately model the effects of environmental toxins on human lungs,” said the Imperial College London.
The newly-launched bioinformatics facility at the National Science Complex in Diliman, Quezon City will enable researchers to undertake super-computing that involves processing of huge volume of data.
“When it comes to scientific computing, you need many processors or computing nodes that will run at the same time. The difference in our facility is we have an IBM machine that is very optimized for minimal energy consumption at a much higher number of processors,” said Arturo O. Lluisma, bioinformatics director, in a separate interview.
While a quad core processor only has four central processors, the IBM BlueGene supercomputer at the PGC bioinformatics facility has hundreds of 4,096 cores.
The Philippine Council for Energy, Industry, and Emerging Technology Research and Development supported acquisition of the IBM BlueGene supercomputer.
The Advanced Science and Technology Institute will provide high-speed connection to the National Computer Center which will host the IBM supercomputer.
Most private companies in the Philippines do have enterprise-grade servers that can be combined in one big cluster for a powerful computing capability.
“But as far as our IBM supercomputer is concerned, that’s the only installation of that kind we have in the Philippines and I think even in Southeast Asia. We have an opportunity to do serious number crunching that wasn’t possible to do before. It can do big genomic data analysis, said Lluisma.
“Genomes of organisms, if you sequence them in their big sizes, would need capacity in the terabytes. The IBM BlueGene will enable us to extract information from that data with its fast system. It will divide work into multiple components, and all the components will be analyzed at the same time.”
The PGC also needs to continue training people in the use of the bioinformatics facility. The IBM BlueGene was acquired for P19 million. Needed to be trained includes statisticians, mathematicians, and physicists.
“The technology is evolving. It’s a matter of keeping abreast of the technology and its progressive enhancement,” Lluisma said.
Padilla said PGC will reach out to academic institutions nationwide and help their experts come up with proposals so that funding will subsequently be obtained for such research proposals.
Under the mentioned NIH research bioengineered organs-on-chips, Tagle said 30 percent of promising medications for diseases fail because these are found to be toxic under human clinical trials. This is despite earlier successful clinical studies in animal models. Other potential drugs, some 60 percent, fail due to efficacy problems.
“The challenge of accurately predicting drug toxicities and efficacies is in part due to inherent species differences in drug metabolizing enzyme activities and cell-type specific sensitivities to toxicants.
This is the reason why NIH put in $70 million for the organs-on-chips program which involves simulation of functions of 10 specific major human organ systems. These are circulatory, respiratory, integumentary, reproductive, endocrine, gastrointestinal, nervous, urinary, musculoskeletal, and immune systems.
“The opportunities for significant advancements in the prediction of human drug toxicities through development of microphysiological systems requires a multi-disciplinary approach that relies on understanding of human physiology, stem cell biology, material sciences, and bioengineering,” said Tagle.